Coalescence: the Sharing of Ancestry of Alleles


Coalescence is the process whereby alleles sampled from a population can be traced back to a single ancestor. When the variation that exists between the alleles is neutral in its effect on Darwinian fitness, the analysis of expected patterns in coalescent processes is simple, due to the independence of the phylogeny of the alleles from the mutational changes that they have undergone. The structure of this genealogy can reveal whether the population has been constant in size and whether it has been geographically subdivided. It can also suggest whether selection has operated, particularly if unexpected patterns are seen at individual genetic loci, and not genome‚Äźwide. However, due to the intrinsically stochastic nature of the coalescent process, inference of demographic changes from a coalescent analysis is difficult, particularly when only one or a few loci are examined.

Key Concepts:

  • Allelic DNA sequences sampled from a population share common ancestry and are connected by a phylogeny.

  • If DNA sequence variation is neutral with respect to natural selection, and if the population has been panmictic and of constant size, the expected phylogenies of alleles are easy to predict.

  • The coalescent process predicts the expected level and distribution of DNA sequence variation in populations.

  • The expected level of variation is determined by the product of the neutral mutation rate and the effective population size.

  • If data from wild populations differ from the expectations of the coalescent process, possible explanations include population subdivision, changes in population size and the action of natural selection.

  • Recombination has the effect that the phylogenies of different genetic loci will be different, although they will be correlated if the loci are linked.

  • Although the demographic history of a population will influence the coalescent process and thus the variation in the alleles sampled from a population, the inherent stochasticity of the process makes it hard to infer demographic histories with confidence from genetic variation, especially if few loci are considered.

Keywords: population genetics; DNA; neutral evolution; polymorphism; gene genealogy

Figure 1.

A typical gene genealogy for five sampled alleles evolving following the neutral coalescent process.

Figure 2.

A gene genealogy showing a deep split and likely to result in a positive value of d.

Figure 3.

A star‐shaped gene genealogy resulting in a negative value of d.



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How to Cite close
Brookfield, John FY(Oct 2011) Coalescence: the Sharing of Ancestry of Alleles. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0001775.pub2]